Origin and fate of repeats in bacteria. - Guillaume Achaz; Eduardo P. C. Rocha; P. Netter; Eric Coissac (Nucleic Acids Res., 2002)

An Integrative Method for Accurate Comparative Genome Mapping. - Firas Swidan; Eduardo P. C. Rocha; Michael Shmoish; Ron Y. Pinter (PLoS Comput. Biol., 2006)

Repseek, a tool to retrieve approximate repeats from large DNA sequences. - Guillaume Achaz; Frédéric Boyer; Eduardo P. C. Rocha; Alain Viari; Eric Coissac (Bioinform., 2007)

Swelfe: a detector of internal repeats in sequences and structures. - Anne-Laure Abraham; Eduardo P. C. Rocha; Joël Pothier (Bioinform., 2008)

Protein evolution driven by symmetric structural repeats. - Anne-Laure Abraham; Joël Pothier; Eduardo P. C. Rocha (BMC Bioinform., 2008)

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Guillaume Achaz; Mark A. Ragan; Xavier Messeguer; Eduardo P. C. Rocha (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. - David Couvin; Aude Bernheim; Claire Toffano-Nioche; Marie Touchon; Juraj Michalik; Bertrand Néron; Eduardo P. C. Rocha; Gilles Vergnaud; Daniel Gautheret; Christine Pourcel (Nucleic Acids Res., 2018)

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. - Guillaume Gautreau; Adelme Bazin; Mathieu Gachet; Rémi Planel; Laura Burlot; Mathieu Dubois; Amandine Perrin; Claudine Médigue; Alexandra Calteau; Stéphane Cruveiller; Catherine Matias; Christophe Ambroise; et al. (PLoS Comput. Biol., 2020)

Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. - Guillaume Gautreau; Adelme Bazin; Mathieu Gachet; Rémi Planel; Laura Burlot; Mathieu Dubois; Amandine Perrin; Claudine Médigue; Alexandra Calteau; Stéphane Cruveiller; Catherine Matias; Christophe Ambroise; et al. (PLoS Comput. Biol., 2021)

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. - Kristen D. Curry; Feiqiao Brian Yu; Summer E. Vance; Santiago Segarra; Devaki Bhaya; Rayan Chikhi; Eduardo P. C. Rocha; Todd J. Treangen (Bioinform., 2024)